@article{Hirashima2003,
abstract = {The compounds 1-(2,6-diethylphenyl)imidazolidine-2-thione and 2-(2,6-diethylphenyl)imidazolidine showed the almost same activity as octopamine in stimulating adenylate cyclase of cockroach thoracic nervous system among 70 octopamine agonists, suggesting that only these compounds are full octopamine agonists and other compounds are partial octopamine agonists. The quantitative structure-activity relationship of a set of 22 octopamine agonists against receptor 2 in cockroach nervous tissue, was analyzed using receptor surface modeling. Three-dimensional energetics descriptors were calculated from receptor surface model/ligand interaction and these three-dimensional descriptors were used in quantitative structure-activity relationship analysis. A receptor surface model was generated using some subset of the most active structures and the results provided useful information in the characterization and differentiation of octopaminergic receptor.},
author = {Hirashima, Akinori and Morimoto, Masako and Kuwano, Eiichi and Eto, Morifusa},
file = {:C$\backslash$:/Users/Draco/Dropbox/octopamine\_receptor/papers/2011-04 - Spring/Octopamine Agonist Paper.pdf:pdf},
issn = {1536-2442},
journal = {Journal of insect science (Online)},
keywords = {Adenylate Cyclase,Adenylate Cyclase: metabolism,Animals,Cockroaches,Cockroaches: drug effects,Cockroaches: metabolism,Ethylenethiourea,Ethylenethiourea: analogs \& derivatives,Ethylenethiourea: chemistry,Female,Imidazolidines,Imidazolidines: agonists,Imidazolidines: chemistry,Male,Models, Molecular,Molecular Structure,Neurons,Neurons: metabolism,Octopamine,Octopamine: agonists,Octopamine: chemistry,Protein Binding,Quantitative Structure-Activity Relationship,Receptors, Biogenic Amine,Receptors, Biogenic Amine: metabolism},
month = jan,
pages = {10},
pmid = {15841226},
title = {{Octopaminergic agonists for the cockroach neuronal octopamine receptor.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=524650\&tool=pmcentrez\&rendertype=abstract},
volume = {3},
year = {2003}
}
@article{Huang2008,
abstract = {Octopamine (OA) is thought to be the invertebrate counterpart of noradrenaline and regulates various behavioral patterns of invertebrates by activating OA receptors. As a typical G protein-coupled receptor, BmOAR1, a Bombyx mori alpha-adrenergic-like OA receptor, is coupled to both G(s) and G(q) proteins to induce the release of the intracellular second messengers cAMP and Ca(2+). In this study, we examined the pharmacological and functional properties of the cloned OA receptor, using OA enantiomers. The wild-type OA receptor exhibited significant stereoselectivity for OA enantiomers in cAMP production and binding affinity, but not in calcium signaling response. On the contrary, the Y412F mutant abolished the discrimination between OA enantiomers in the binding affinity and did not evoke any cAMP signaling response. This mutant exhibited levels of potency and efficacy similar to those of the wild-type receptor in the calcium assays. Taken together, these results suggest that Tyr412 might act as a molecular switch to regulate distinct G protein couplings, and a sequential activation model is proposed for such specific-residue-dependent, selective activation in receptors that are coupled to multiple G proteins.},
author = {Huang, Jia and Hamasaki, Tomohiro and Ozoe, Fumiyo and Ozoe, Yoshihisa},
doi = {10.1016/j.bbrc.2008.03.135},
file = {:C$\backslash$:/Users/Draco/Dropbox/octopamine\_receptor/papers/2011-04 - Spring/Octopamine docking.pdf:pdf},
issn = {1090-2104},
journal = {Biochemical and biophysical research communications},
keywords = {Amino Acid Substitution,Animals,Bombyx,Cell Line,GTP-Binding Proteins,GTP-Binding Proteins: metabolism,Humans,Models, Molecular,Octopamine,Octopamine: pharmacology,Protein Conformation,Receptors, Biogenic Amine,Receptors, Biogenic Amine: chemistry,Receptors, Biogenic Amine: genetics,Receptors, Biogenic Amine: metabolism,Tyrosine,Tyrosine: chemistry,Tyrosine: metabolism},
month = jul,
number = {4},
pages = {610--4},
pmid = {18395516},
title = {{Single amino acid of an octopamine receptor as a molecular switch for distinct G protein couplings.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18395516},
volume = {371},
year = {2008}
}
@article{Hirashim2002,
abstract = {Three-dimensional pharmacophore hypotheses were built from a set of 12 octopamine (OA) agonist arylethanolamines (AEAs). Among the 10 common-featured models generated by program catalyst/HipHop, a hypothesis including a hydrogen-bond donor (HBD) and a hydrogen-bond acceptor lipid (HBA1) features was considered to be important in evaluating the OA activity. OA mapped well onto all the HBD and HBA1 features of the hypothesis. On the other hand, for some inactive compounds, their lack of affinity is primarily due to their inability to achieve an energetically favorable conformation shared by the active compounds. Taken together, structures of a 4-OH-Ph, alpha-OH, and a primary amine are important for OA activities. The present studies on OA agonists demonstrate that an HBD and an HBA1 sites located on the molecule seem to be essential for OA activity.},
author = {Hirashim, Akinori and Morimoto, Masako and Kuwano, Eiichi and Taniguchi, Eiji and Eto, Morifusa},
file = {:C$\backslash$:/Users/Draco/Dropbox/octopamine\_receptor/papers/2011-04 - Spring/Pharmacophore Modeling of Octopamine analogs.pdf:pdf},
issn = {1093-3263},
journal = {Journal of molecular graphics \& modelling},
keywords = {Adrenergic alpha-Agonists,Adrenergic alpha-Agonists: chemistry,Animals,Cyclic AMP,Cyclic AMP: metabolism,Drug Design,Ethanolamines,Ethanolamines: chemical synthesis,Ethanolamines: chemistry,Female,Hydrogen Bonding,Male,Models, Molecular,Molecular Structure,Octopamine,Octopamine: agonists,Octopamine: chemistry,Periplaneta,Periplaneta: chemistry},
month = oct,
number = {2},
pages = {81--7},
pmid = {12398339},
title = {{Three-dimensional common-feature hypotheses for octopamine agonist arylethanolamines.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/12398339},
volume = {21},
year = {2002}
}
@article{Rasmussen2011,
abstract = {G protein coupled receptors (GPCRs) exhibit a spectrum of functional behaviours in response to natural and synthetic ligands. Recent crystal structures provide insights into inactive states of several GPCRs. Efforts to obtain an agonist-bound active-state GPCR structure have proven difficult due to the inherent instability of this state in the absence of a G protein. We generated a camelid antibody fragment (nanobody) to the human $\beta$2 adrenergic receptor ($\beta$2AR) that exhibits G protein-like behaviour, and obtained an agonist-bound, active-state crystal structure of the receptor-nanobody complex. Comparison with the inactive $\beta$2AR structure reveals subtle changes in the binding pocket; however, these small changes are associated with an 11 \AA outward movement of the cytoplasmic end of transmembrane segment 6, and rearrangements of transmembrane segments 5 and 7 that are remarkably similar to those observed in opsin, an active form of rhodopsin. This structure provides insights into the process of agonist binding and activation.},
author = {Rasmussen, S\o ren G. F. and Choi, Hee-Jung and Fung, Juan Jose and Pardon, Els and Casarosa, Paola and Chae, Pil Seok and DeVree, Brian T. and Rosenbaum, Daniel M. and Thian, Foon Sun and Kobilka, Tong Sun and Schnapp, Andreas and Konetzki, Ingo and Sunahara, Roger K. and Gellman, Samuel H. and Pautsch, Alexander and Steyaert, Jan and Weis, William I. and Kobilka, Brian K.},
doi = {10.1038/nature09648},
file = {:C$\backslash$:/Users/Draco/Dropbox/octopamine\_receptor/papers/2011-04 - Spring/Rasmussen\_2011\_Nature.pdf:pdf},
issn = {0028-0836},
journal = {Nature},
month = jan,
number = {7329},
pages = {175--180},
publisher = {Nature Publishing Group},
title = {{Structure of a nanobody-stabilized active state of the $\beta$2 adrenoceptor}},
url = {http://www.nature.com/doifinder/10.1038/nature09648},
volume = {469},
year = {2011}
}
@article{,
file = {:C$\backslash$:/Users/Draco/Dropbox/octopamine\_receptor/papers/2011-04 - Spring/struct.pdf:pdf},
pages = {1--143},
title = {{LOPAC1280.db}}
}
@article{Rosenbaum2011,
abstract = {G-protein-coupled receptors (GPCRs) are eukaryotic integral membrane proteins that modulate biological function by initiating cellular signalling in response to chemically diverse agonists. Despite recent progress in the structural biology of GPCRs, the molecular basis for agonist binding and allosteric modulation of these proteins is poorly understood. Structural knowledge of agonist-bound states is essential for deciphering the mechanism of receptor activation, and for structure-guided design and optimization of ligands. However, the crystallization of agonist-bound GPCRs has been hampered by modest affinities and rapid off-rates of available agonists. Using the inactive structure of the human $\beta$(2) adrenergic receptor ($\beta$(2)AR) as a guide, we designed a $\beta$(2)AR agonist that can be covalently tethered to a specific site on the receptor through a disulphide bond. The covalent $\beta$(2)AR-agonist complex forms efficiently, and is capable of activating a heterotrimeric G protein. We crystallized a covalent agonist-bound $\beta$(2)AR-T4L fusion protein in lipid bilayers through the use of the lipidic mesophase method, and determined its structure at 3.5 \AA resolution. A comparison to the inactive structure and an antibody-stabilized active structure (companion paper) shows how binding events at both the extracellular and intracellular surfaces are required to stabilize an active conformation of the receptor. The structures are in agreement with long-timescale (up to 30 $\mu$s) molecular dynamics simulations showing that an agonist-bound active conformation spontaneously relaxes to an inactive-like conformation in the absence of a G protein or stabilizing antibody.},
author = {Rosenbaum, Daniel M and Zhang, Cheng and Lyons, Joseph a and Holl, Ralph and Aragao, David and Arlow, Daniel H and Rasmussen, S\o ren G F and Choi, Hee-Jung and Devree, Brian T and Sunahara, Roger K and Chae, Pil Seok and Gellman, Samuel H and Dror, Ron O and Shaw, David E and Weis, William I and Caffrey, Martin and Gmeiner, Peter and Kobilka, Brian K},
doi = {10.1038/nature09665},
file = {:C$\backslash$:/Users/Draco/Dropbox/octopamine\_receptor/papers/2011-04 - Spring/Rosenbaum\_2104\_Nature.pdf:pdf},
issn = {1476-4687},
journal = {Nature},
keywords = {Adrenergic beta-2 Receptor Agonists,Adrenergic beta-2 Receptor Agonists: chemistry,Adrenergic beta-2 Receptor Agonists: metabolism,Crystallization,Crystallography, X-Ray,Disulfides,Disulfides: chemistry,Disulfides: metabolism,Drug Inverse Agonism,Heterotrimeric GTP-Binding Proteins,Heterotrimeric GTP-Binding Proteins: metabolism,Humans,Lipid Bilayers,Lipid Bilayers: chemistry,Lipid Bilayers: metabolism,Models, Molecular,Molecular Dynamics Simulation,Procaterol,Procaterol: chemistry,Procaterol: metabolism,Propanolamines,Propanolamines: chemistry,Propanolamines: metabolism,Protein Conformation,Receptors, Adrenergic, beta-2,Receptors, Adrenergic, beta-2: chemistry,Receptors, Adrenergic, beta-2: metabolism,Recombinant Fusion Proteins,Recombinant Fusion Proteins: chemistry,Recombinant Fusion Proteins: metabolism,Viral Proteins,Viral Proteins: chemistry,Viral Proteins: metabolism},
month = jan,
number = {7329},
pages = {236--40},
pmid = {21228876},
publisher = {Nature Publishing Group},
title = {{Structure and function of an irreversible agonist-$\beta$(2) adrenoceptor complex.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3074335\&tool=pmcentrez\&rendertype=abstract},
volume = {469},
year = {2011}
}
@article{Hirashima2002,
abstract = {Three-dimensional pharmacophore hypotheses were built from a set of 10 octopamine (OA) agonist 2-(Arylimino)imidazolidines (AIIs), 2-(Arylimino)thiazolidines (AITs) and 2-(Arylimino)oxazolidines (AIOs). Among the 10 common-featured models generated by program Catalyst/HipHop, a hypothesis including a ring aromatic (RA), a positive ionizable (PI) and three hydrophobic aliphatic (HpAl) features was considered to be important in evaluating the OA-agonist activity. Active OA agonist 2,6-Et2 AII mapped well onto all the RA, PI and HpAl features of the hypothesis. On the other hand, less active compounds were shown to be difficult to achieve the energetically favorable conformation which is found in the active molecules in order to fit the 3-D common-feature pharmacophore models. Taken together, 2,6-Et2-Ph and foramidine structures are important as OA agonists. The present studies on OA agonists demonstrate that a RA, a PI and three HpAl sites located on the molecule seem to be essential for OA-agonist activity.},
author = {Hirashima, Akinori and Morimoto, Masako and Kuwano, Eiichi and Taniguchi, Eiji and Eto, Morifusa},
file = {:C$\backslash$:/Users/Draco/Dropbox/octopamine\_receptor/papers/2011-04 - Spring/Three-Dimensional Common Features of Octopamine Agonists.pdf:pdf},
issn = {0968-0896},
journal = {Bioorganic \& medicinal chemistry},
keywords = {Animals,Catalysis,Cockroaches,Cockroaches: drug effects,Female,Imidazoles,Imidazoles: chemistry,Imidazoles: pharmacology,Male,Octopamine,Octopamine: agonists},
month = jan,
number = {1},
pages = {117--23},
pmid = {11738614},
title = {{Three-dimensional common-feature hypotheses for octopamine agonist 2-(arylimino)imidazolidines.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/11738614},
volume = {10},
year = {2002}
}
@article{Grossfield2011,
abstract = {G protein-coupled receptors (GPCRs) are a large, biomedically important family of proteins, and the recent explosion of new high-resolution structural information about them has provided an enormous opportunity for computational modeling to make major contributions. In particular, molecular dynamics simulations have become a driving factor in many areas of GPCR biophysics, improving our understanding of lipid-protein interaction, activation mechanisms, and internal hydration. Given that computers will continue to get faster and more structures will be solved, the importance of computational methods will only continue to grow, particularly as simulation research is more closely coupled to experiment.},
author = {Grossfield, Alan},
doi = {10.1016/j.bbamem.2011.03.010},
file = {:C$\backslash$:/Users/Draco/Dropbox/octopamine\_receptor/papers/2011-05 - May/Grossfield (2011) - Recent progress of GPCR with MD sims.pdf:pdf},
issn = {0006-3002},
journal = {Biochimica et biophysica acta},
keywords = {Biopolymers,Biopolymers: chemistry,Computer Simulation,Lipids,Lipids: chemistry,Models, Molecular,Molecular Dynamics Simulation,Receptors, G-Protein-Coupled,Receptors, G-Protein-Coupled: chemistry,Schiff Bases},
month = jul,
number = {7},
pages = {1868--78},
pmid = {21443858},
publisher = {Elsevier B.V.},
title = {{Recent progress in the study of G protein-coupled receptors with molecular dynamics computer simulations.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21443858},
volume = {1808},
year = {2011}
}
@article{Chiang2011,
abstract = {Loss-of-function mutations in the gene encoding G protein-coupled receptor 56 (GPR56) lead to bilateral frontoparietal polymicrogyria (BFPP), an autosomal recessive disorder affecting brain development. The GPR56 receptor is a member of the adhesion-GPCR family characterized by the chimeric composition of a long ectodomain (ECD), a GPCR proteolysis site (GPS), and a seven-pass transmembrane (7TM) moiety. Interestingly, all identified BFPP-associated missense mutations are located within the extracellular region of GPR56 including the ECD, GPS, and the extracellular loops of 7TM. In the present study, a detailed molecular and functional analysis of the wild-type GPR56 and BFPP-associated point mutants shows that individual GPR56 mutants most likely cause BFPP via different combination of multiple mechanisms. These include reduced surface receptor expression, loss of GPS proteolysis, reduced receptor shedding, inability to interact with a novel protein ligand, and differential distribution of the 7TM moiety in lipid rafts. These results provide novel insights into the cellular functions of GPR56 receptor and reveal molecular mechanisms whereby GPR56 mutations induce BFPP.},
author = {Chiang, Nien-Yi and Hsiao, Cheng-Chih and Huang, Yi-Shu and Chen, Hsin-Yi and Hsieh, I-Ju and Chang, Gin-Wen and Lin, Hsi-Hsien},
doi = {10.1074/jbc.M110.183830},
file = {:C$\backslash$:/Users/Draco/Dropbox/octopamine\_receptor/papers/2011-05 - May/J. Biol. Chem.-2011-Chiang-14215-25.pdf:pdf},
issn = {1083-351X},
journal = {The Journal of biological chemistry},
keywords = {Animals,CHO Cells,Cricetinae,Cricetulus,Glycosaminoglycans,Glycosaminoglycans: chemistry,Humans,Malformations of Cortical Development,Malformations of Cortical Development: genetics,Membrane Microdomains,Mice,Nervous System Diseases,Nervous System Diseases: metabolism,Point Mutation,Protein Binding,Receptors, G-Protein-Coupled,Receptors, G-Protein-Coupled: genetics,Receptors, G-Protein-Coupled: metabolism,Receptors, G-Protein-Coupled: physiology},
month = apr,
number = {16},
pages = {14215--25},
pmid = {21349848},
title = {{Disease-associated GPR56 mutations cause bilateral frontoparietal polymicrogyria via multiple mechanisms.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3077623\&tool=pmcentrez\&rendertype=abstract},
volume = {286},
year = {2011}
}
@article{Jastrzebska2011,
abstract = {Rhodopsin is a prototypical G protein-coupled receptor (GPCR) - a member of the superfamily that shares a similar structural architecture consisting of seven-transmembrane helices and propagates various signals across biological membranes. Rhodopsin is embedded in the lipid bilayer of specialized disk membranes in the outer segments of retinal rod photoreceptor cells where it transmits a light-stimulated signal. Photoactivated rhodopsin then activates a visual signaling cascade through its cognate G protein, transducin or Gt, that results in a neuronal response in the brain. Interestingly, the lipid composition of ROS membranes not only differs from that of the photoreceptor plasma membrane but is critical for visual transduction. Specifically, lipids can modulate structural changes in rhodopsin that occur after photoactivation and influence binding of transducin. Thus, altering the lipid organization of ROS membranes can result in visual dysfunction and blindness.},
author = {Jastrzebska, Beata and Debinski, Aleksander and Filipek, Slawomir and Palczewski, Krzysztof},
doi = {10.1016/j.plipres.2011.03.002},
file = {:C$\backslash$:/Users/Draco/Dropbox/octopamine\_receptor/papers/2011-05 - May/Jastrzebska (2011) - Role of membrane integrity on GPCRs.pdf:pdf},
issn = {1873-2194},
journal = {Progress in lipid research},
keywords = {g protein-coupled receptor,s},
month = jul,
number = {3},
pages = {267--77},
pmid = {21435354},
publisher = {Elsevier Ltd},
title = {{Role of membrane integrity on G protein-coupled receptors: Rhodopsin stability and function.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3114187\&tool=pmcentrez\&rendertype=abstract},
volume = {50},
year = {2011}
}
@article{Johnston2011,
abstract = {Opioid receptors, like other members of the G protein-coupled receptor (GPCR) family, have been shown to associate to form dimers and/or oligomers at the plasma membrane. Whether this association is stable or transient is not known. Recent compelling evidence suggests that at least some GPCRs rapidly associate and dissociate. We have recently calculated binding affinities from free energy estimates to predict transient association between mouse delta opioid receptor (DOR) protomers at a symmetric interface involving the fourth transmembrane (TM4) helix (herein termed "4" dimer). Here we present disulfide cross-linking experiments with DOR constructs with cysteines substituted at the extracellular ends of TM4 or TM5 that confirm the formation of DOR complexes involving these helices. Our results are consistent with the involvement of TM4 and/or TM5 at the DOR homodimer interface, but possibly with differing association propensities. Coarse-grained (CG) well-tempered metadynamics simulations of two different dimeric arrangements of DOR involving TM4 alone or with TM5 (herein termed "4/5" dimer) in an explicit lipid-water environment confirmed the presence of two structurally and energetically similar configurations of the 4 dimer, as previously assessed by umbrella sampling calculations, and revealed a single energetic minimum of the 4/5 dimer. Additional CG umbrella sampling simulations of the 4/5 dimer indicated that the strength of association between DOR protomers varies depending on the protein region at the interface, with the 4 dimer being more stable than the 4/5 dimer.},
author = {Johnston, Jennifer M and Aburi, Mahalaxmi and Provasi, Davide and Bortolato, Andrea and Urizar, Eneko and Lambert, Nevin a and Javitch, Jonathan a and Filizola, Marta},
doi = {10.1021/bi101474v},
file = {:C$\backslash$:/Users/Draco/Dropbox/octopamine\_receptor/papers/2011-05 - May/Johnston (2011) - Dimerization Interfaces of Delta Opioid Receptor.pdf:pdf},
issn = {1520-4995},
journal = {Biochemistry},
keywords = {Animals,HEK293 Cells,Humans,Mice,Models, Molecular,Protein Multimerization,Protein Structure, Quaternary,Receptors, Opioid, delta,Receptors, Opioid, delta: chemistry,Receptors, Opioid, delta: metabolism},
month = mar,
number = {10},
pages = {1682--90},
pmid = {21261298},
title = {{Making structural sense of dimerization interfaces of delta opioid receptor homodimers.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3050604\&tool=pmcentrez\&rendertype=abstract},
volume = {50},
year = {2011}
}
@article{Kuo2004,
abstract = {From the deductive point of view, neurotransmitter receptors can be divided into categories such as cholinergic (muscarinic, nicotinic), adrenergic (alpha- and beta-), dopaminergic, serotoninergic (5-HT1 approximately 5-HT5), and histaminergic (H1 and H2). Selective agonists and antagonists of each receptor subtype can have specific useful therapeutic applications. For understanding the molecular mechanisms of action, an inductive method of analysis is useful.},
author = {Kuo, C L and Wang, R B and Shen, L J and Lien, L L and Lien, E J},
doi = {10.1111/j.1365-2710.2004.00563.x},
file = {:C$\backslash$:/Users/Draco/Dropbox/octopamine\_receptor/papers/2011-05 - May/Kuo et al (2004) - GPCRs, SAR analyses.pdf:pdf},
isbn = {3234421390},
issn = {0269-4727},
journal = {Journal of clinical pharmacy and therapeutics},
keywords = {Adrenergic Agonists,Adrenergic Agonists: chemistry,Adrenergic Agonists: classification,Adrenergic Antagonists,Adrenergic Antagonists: chemistry,Adrenergic Antagonists: classification,Chemistry, Physical,Cholinergic Agonists,Cholinergic Agonists: chemistry,Cholinergic Agonists: classification,Cholinergic Antagonists,Cholinergic Antagonists: chemistry,Cholinergic Antagonists: classification,Dopamine Agonists,Dopamine Agonists: chemistry,Dopamine Agonists: classification,Dopamine Agonists: pharmacology,Dopamine Antagonists,Dopamine Antagonists: chemistry,Dopamine Antagonists: classification,Dopamine Antagonists: pharmacology,Histamine Agonists,Histamine Agonists: chemistry,Histamine Agonists: classification,Histamine Agonists: pharmacology,Histamine Antagonists,Histamine Antagonists: chemistry,Histamine Antagonists: classification,Histamine Antagonists: pharmacology,Models, Biological,Molecular Structure,Neurotransmitter Agents,Neurotransmitter Agents: agonists,Neurotransmitter Agents: antagonists \& inhibitors,Neurotransmitter Agents: chemistry,Physicochemical Phenomena,Receptors, Adrenergic,Receptors, Adrenergic: classification,Receptors, Adrenergic: drug effects,Receptors, Adrenergic: physiology,Receptors, Cholinergic,Receptors, Cholinergic: classification,Receptors, Cholinergic: drug effects,Receptors, Cholinergic: physiology,Receptors, G-Protein-Coupled,Receptors, G-Protein-Coupled: drug effects,Receptors, G-Protein-Coupled: physiology,Receptors, Histamine,Receptors, Histamine: classification,Receptors, Histamine: drug effects,Receptors, Histamine: physiology,Serotonin Antagonists,Serotonin Antagonists: chemistry,Serotonin Antagonists: classification,Serotonin Antagonists: pharmacology,Serotonin Receptor Agonists,Serotonin Receptor Agonists: chemistry,Serotonin Receptor Agonists: classification,Serotonin Receptor Agonists: pharmacology,Structure-Activity Relationship},
month = jun,
number = {3},
pages = {279--98},
pmid = {15153091},
title = {{G-protein coupled receptors: SAR analyses of neurotransmitters and antagonists.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15153091},
volume = {29},
year = {2004}
}
@article{Nishimasu2011,
abstract = {Autotaxin (ATX, also known as Enpp2) is a secreted lysophospholipase D that hydrolyzes lysophosphatidylcholine to generate lysophosphatidic acid (LPA), a lipid mediator that activates G protein-coupled receptors to evoke various cellular responses. Here, we report the crystal structures of mouse ATX alone and in complex with LPAs with different acyl-chain lengths and saturations. These structures reveal that the multidomain architecture helps to maintain the structural rigidity of the lipid-binding pocket, which accommodates the respective LPA molecules in distinct conformations. They indicate that a loop region in the catalytic domain is a major determinant for the substrate specificity of the Enpp family enzymes. Furthermore, along with biochemical and biological data, these structures suggest that the produced LPAs are delivered from the active site to cognate G protein-coupled receptors through a hydrophobic channel.},
author = {Nishimasu, Hiroshi and Okudaira, Shinichi and Hama, Kotaro and Mihara, Emiko and Dohmae, Naoshi and Inoue, Asuka and Ishitani, Ryuichiro and Takagi, Junichi and Aoki, Junken and Nureki, Osamu},
doi = {10.1038/nsmb.1998},
file = {:C$\backslash$:/Users/Draco/Dropbox/octopamine\_receptor/papers/2011-05 - May/Nishimasu (2011) - Insight into GPCR activation by lipid mediators.pdf:pdf},
issn = {1545-9985},
journal = {Nature structural \& molecular biology},
keywords = {Amino Acid Sequence,Animals,Binding Sites,Cell Line,Crystallography, X-Ray,Humans,Hydrophobic and Hydrophilic Interactions,Lysophospholipids,Lysophospholipids: chemistry,Lysophospholipids: metabolism,Mice,Models, Molecular,Molecular Sequence Data,Multienzyme Complexes,Multienzyme Complexes: chemistry,Multienzyme Complexes: metabolism,Phosphodiesterase I,Phosphodiesterase I: chemistry,Phosphodiesterase I: metabolism,Protein Conformation,Pyrophosphatases,Pyrophosphatases: chemistry,Pyrophosphatases: metabolism,Receptors, G-Protein-Coupled,Receptors, G-Protein-Coupled: metabolism,Substrate Specificity},
month = feb,
number = {2},
pages = {205--12},
pmid = {21240269},
publisher = {Nature Publishing Group},
title = {{Crystal structure of autotaxin and insight into GPCR activation by lipid mediators.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21240269},
volume = {18},
year = {2011}
}
@article{Hall2011,
abstract = {The interaction of $\alpha$-helical peptides with lipid bilayers is central to our understanding of the physicochemical principles of biological membrane organization and stability. Mutations that alter the position or orientation of an $\alpha$-helix within a membrane, or that change the probability that the $\alpha$-helix will insert into the membrane, can alter a range of membrane protein functions. We describe a comparative coarse-grained molecular dynamics simulation methodology, based on self-assembly of a lipid bilayer in the presence of an $\alpha$-helical peptide, which allows us to model membrane transmembrane helix insertion. We validate this methodology against available experimental data for synthetic model peptides (WALP23 and LS3). Simulation-based estimates of apparent free energies of insertion into a bilayer of cystic fibrosis transmembrane regulator-derived helices correlate well with published data for translocon-mediated insertion. Comparison of values of the apparent free energy of insertion from self-assembly simulations with those from coarse-grained molecular dynamics potentials of mean force for model peptides, and with translocon-mediated insertion of cystic fibrosis transmembrane regulator-derived peptides suggests a nonequilibrium model of helix insertion into bilayers.},
author = {Hall, Benjamin a and Chetwynd, Alan P and Sansom, Mark S P},
doi = {10.1016/j.bpj.2011.02.041},
file = {:C$\backslash$:/Users/Draco/Dropbox/octopamine\_receptor/papers/2011-05 - May/SansomBJ11[Coarse Grain Peptide-Membrane].pdf:pdf},
issn = {1542-0086},
journal = {Biophysical journal},
month = apr,
number = {8},
pages = {1940--8},
pmid = {21504730},
publisher = {Biophysical Society},
title = {{Exploring peptide-membrane interactions with coarse-grained MD simulations.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3077683\&tool=pmcentrez\&rendertype=abstract},
volume = {100},
year = {2011}
}
@article{Chien2010,
abstract = {Dopamine modulates movement, cognition, and emotion through activation of dopamine G protein-coupled receptors in the brain. The crystal structure of the human dopamine D3 receptor (D3R) in complex with the small molecule D2R/D3R-specific antagonist eticlopride reveals important features of the ligand binding pocket and extracellular loops. On the intracellular side of the receptor, a locked conformation of the ionic lock and two distinctly different conformations of intracellular loop 2 are observed. Docking of R-22, a D3R-selective antagonist, reveals an extracellular extension of the eticlopride binding site that comprises a second binding pocket for the aryl amide of R-22, which differs between the highly homologous D2R and D3R. This difference provides direction to the design of D3R-selective agents for treating drug abuse and other neuropsychiatric indications.},
author = {Chien, Ellen Y T and Liu, Wei and Zhao, Qiang and Katritch, Vsevolod and Han, Gye Won and Hanson, Michael a and Shi, Lei and Newman, Amy Hauck and Javitch, Jonathan a and Cherezov, Vadim and Stevens, Raymond C},
doi = {10.1126/science.1197410},
file = {:C$\backslash$:/Users/Draco/Dropbox/octopamine\_receptor/papers/2011-06 - June/d03\_science.pdf:pdf},
issn = {1095-9203},
journal = {Science (New York, N.Y.)},
keywords = {Animals,Arginine,Arginine: chemistry,Binding Sites,Cell Line,Crystallography, X-Ray,Dopamine Antagonists,Dopamine Antagonists: chemistry,Humans,Models, Molecular,Protein Conformation,Receptors, Dopamine D2,Receptors, Dopamine D2: antagonists \& inhibitors,Receptors, Dopamine D3,Receptors, Dopamine D3: antagonists \& inhibitors,Receptors, Dopamine D3: chemistry,Recombinant Proteins,Recombinant Proteins: chemistry,Salicylamides,Salicylamides: chemistry,Spodoptera},
month = nov,
number = {6007},
pages = {1091--5},
pmid = {21097933},
title = {{Structure of the human dopamine D3 receptor in complex with a D2/D3 selective antagonist.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3058422\&tool=pmcentrez\&rendertype=abstract},
volume = {330},
year = {2010}
}
@article{Kalani2004,
abstract = {Dopamine neurotransmitter and its receptors play a critical role in the cell signaling process responsible for information transfer in neurons functioning in the nervous system. Development of improved therapeutics for such disorders as Parkinson's disease and schizophrenia would be significantly enhanced with the availability of the 3D structure for the dopamine receptors and of the binding site for dopamine and other agonists and antagonists. We report here the 3D structure of the long isoform of the human D2 dopamine receptor, predicted from primary sequence using first-principles theoretical and computational techniques (i.e., we did not use bioinformatic or experimental 3D structural information in predicting structures). The predicted 3D structure is validated by comparison of the predicted binding site and the relative binding affinities of dopamine, three known dopamine agonists (antiparkinsonian), and seven known antagonists (antipsychotic) in the D2 receptor to experimentally determined values. These structures correctly predict the critical residues for binding dopamine and several antagonists, identified by mutation studies, and give relative binding affinities that correlate well with experiments. The predicted binding site for dopamine and agonists is located between transmembrane (TM) helices 3, 4, 5, and 6, whereas the best antagonists bind to a site involving TM helices 2, 3, 4, 6, and 7 with minimal contacts to TM helix 5. We identify characteristic differences between the binding sites of agonists and antagonists.},
author = {Kalani, M Yashar S and Vaidehi, Nagarajan and Hall, Spencer E and Trabanino, Rene J and Freddolino, Peter L and Kalani, Maziyar a and Floriano, Wely B and Kam, Victor Wai Tak and Goddard, William a},
doi = {10.1073/pnas.0400100101},
file = {:C$\backslash$:/Users/Draco/Dropbox/octopamine\_receptor/papers/2011-06 - June/dopamine\_structure.pdf:pdf},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
keywords = {Binding Sites,Computational Biology,Dopamine Agonists,Dopamine Agonists: metabolism,Dopamine Antagonists,Dopamine Antagonists: metabolism,Humans,Ligands,Protein Structure, Tertiary,Receptors, Dopamine,Receptors, Dopamine: chemistry,Receptors, Dopamine: metabolism},
month = mar,
number = {11},
pages = {3815--20},
pmid = {14999101},
title = {{The predicted 3D structure of the human D2 dopamine receptor and the binding site and binding affinities for agonists and antagonists.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=374327\&tool=pmcentrez\&rendertype=abstract},
volume = {101},
year = {2004}
}
@article{Roeder1990,
author = {Roeder, Thomas},
doi = {10.1016/0014-2999(90)94151-M},
file = {:C$\backslash$:/Users/Draco/Dropbox/octopamine\_receptor/papers/2011-06 - June/Mianserin Octopamine Paper.pdf:pdf},
issn = {00142999},
journal = {European Journal of Pharmacology},
month = nov,
number = {2},
pages = {221--224},
title = {{High-affinity antagonists of the locust neuronal octopamine receptor}},
url = {http://linkinghub.elsevier.com/retrieve/pii/001429999094151M},
volume = {191},
year = {1990}
}
@article{Carlsson2011,
abstract = {G protein-coupled receptors (GPCRs) are intensely studied as drug targets and for their role in signaling. With the determination of the first crystal structures, interest in structure-based ligand discovery increased. Unfortunately, for most GPCRs no experimental structures are available. The determination of the D(3) receptor structure and the challenge to the community to predict it enabled a fully prospective comparison of ligand discovery from a modeled structure versus that of the subsequently released crystal structure. Over 3.3 million molecules were docked against a homology model, and 26 of the highest ranking were tested for binding. Six had affinities ranging from 0.2 to 3.1 $\mu$M. Subsequently, the crystal structure was released and the docking screen repeated. Of the 25 compounds selected, five had affinities ranging from 0.3 to 3.0 $\mu$M. One of the new ligands from the homology model screen was optimized for affinity to 81 nM. The feasibility of docking screens against modeled GPCRs more generally is considered.},
author = {Carlsson, Jens and Coleman, Ryan G and Setola, Vincent and Irwin, John J and Fan, Hao and Schlessinger, Avner and Sali, Andrej and Roth, Bryan L and Shoichet, Brian K},
doi = {10.1038/nchembio.662},
file = {:C$\backslash$:/Users/Draco/Dropbox/octopamine\_receptor/papers/2011-09 - September/D3\_docking.pdf:pdf},
issn = {1552-4469},
journal = {Nature chemical biology},
month = sep,
number = {septeMBer},
pages = {1--10},
pmid = {21926995},
publisher = {Nature Publishing Group},
title = {{Ligand discovery from a dopamine D(3) receptor homology model and crystal structure.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21926995},
year = {2011}
}
@article{Newman2009,
author = {Newman, A.H. and Grundt, Peter and Cyriac, George and Deschamps, J.R. and Taylor, Michelle and Kumar, Rakesh and Ho, David and Luedtke, R.R.},
file = {:C$\backslash$:/Users/Draco/Dropbox/octopamine\_receptor/papers/2011-09 - September/D3selective.pdf:pdf},
journal = {Journal of medicinal chemistry},
number = {8},
pages = {2559--2570},
publisher = {ACS Publications},
title = {{N-(4-(4-(2, 3-Dichloro-or 2-methoxyphenyl) piperazin-1-yl) butyl) heterobiarylcarboxamides with Functionalized Linking Chains as High Affinity and Enantioselective D3 Receptor Antagonists}},
url = {http://pubs.acs.org/doi/abs/10.1021/jm900095y},
volume = {52},
year = {2009}
}
@article{Kufareva2011,
abstract = {The community-wide GPCR Dock assessment is conducted to evaluate the status of molecular modeling and ligand docking for human G protein-coupled receptors. The present round of the assessment was based on the recent structures of dopamine D3 and CXCR4 chemokine receptors bound to small molecule antagonists and CXCR4 with a synthetic cyclopeptide. Thirty-five groups submitted their receptor-ligand complex structure predictions prior to the release of the crystallographic coordinates. With closely related homology modeling templates, as for dopamine D3 receptor, and with incorporation of biochemical and QSAR data, modern computational techniques predicted complex details with accuracy approaching experimental. In contrast, CXCR4 complexes that had less-characterized interactions and only distant homology to the known GPCR structures still remained very challenging. The assessment results provide guidance for modeling and crystallographic communities in method development and target selection for further expansion of the structural coverage of the GPCR universe.},
author = {Kufareva, Irina and Rueda, Manuel and Katritch, Vsevolod and Stevens, Raymond C and Abagyan, Ruben},
doi = {10.1016/j.str.2011.05.012},
file = {:C$\backslash$:/Users/Draco/Dropbox/octopamine\_receptor/papers/2011-09 - September/GPCR Modeling and Docking as Reflected by Community-wide GPCR Dock 2010 Assessment.pdf:pdf},
issn = {1878-4186},
journal = {Structure (London, England : 1993)},
month = aug,
number = {8},
pages = {1108--26},
pmid = {21827947},
publisher = {Elsevier Ltd},
title = {{Status of GPCR Modeling and Docking as Reflected by Community-wide GPCR Dock 2010 Assessment.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21827947},
volume = {19},
year = {2011}
}
@article{Congreve2011,
author = {Congreve, Miles and Langmead, Christopher J and Mason, Jonathan S and Marshall, Fiona H},
doi = {10.1021/jm200371q},
file = {:C$\backslash$:/Users/Draco/Dropbox/octopamine\_receptor/papers/2011-09 - September/jm200371q.pdf:pdf},
issn = {1520-4804},
journal = {Journal of medicinal chemistry},
keywords = {Allosteric Regulation,Animals,Binding Sites,Drug Design,Humans,Ligands,Models, Molecular,Protein Conformation,Receptors, G-Protein-Coupled,Receptors, G-Protein-Coupled: agonists,Receptors, G-Protein-Coupled: antagonists \& inhibi,Receptors, G-Protein-Coupled: chemistry},
month = jul,
number = {13},
pages = {4283--311},
pmid = {21615150},
title = {{Progress in structure based drug design for G protein-coupled receptors.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21615150},
volume = {54},
year = {2011}
}
